
% ----------------------------------------------------------------------
%                   LATEX TEMPLATE FOR PhD THESIS
% ----------------------------------------------------------------------

% based on Harish Bhanderi's PhD/MPhil template, then Uni Cambridge
% http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/ThesisStyle/
% corrected and extended in 2007 by Jakob Suckale, then MPI-CBG PhD programme
% and made available through OpenWetWare.org - the free biology wiki


%: Style file for Latex
% Most style definitions are in the external file PhDthesisPSnPDF.
% In this template package, it can be found in ./Latex/Classes/
%\documentclass[twoside,11pt]{Latex/Classes/PhDthesisPSnPDF}
%\include{Latex/Macros/MacroFile1}
\documentclass[oneside,12pt]{Latex/Classes/PhDthesisPSnPDF}
\externaldocument{0_frontmatter/glossary}
\externaldocument{2/chapter_2}
\externaldocument{3/chapter_3}
\externaldocument{4/chapter_4}
\externaldocument{5/chapter_5}
\usepackage[T1]{fontenc}
\usepackage[english]{babel}

\include{Latex/Macros/MacroFile1}
\makeindex



% ----------------------------------------------------------------------
       
% turn of those nasty overfull and underfull hboxes
\hbadness=10000
\hfuzz=50pt



%: --------------------------------------------------------------
%:                  FRONT MATTER: dedications, abstract,..
% --------------------------------------------------------------

\begin{document}
\setpagewiselinenumbers
\modulolinenumbers[5]
\linenumbers
\newif\ifrefs
\refsfalse

%\language{english}

% sets line spacing
\renewcommand\baselinestretch{1.2}
\baselineskip=18pt plus1pt


%: ----------------------- generate cover page ------------------------

%\maketitle  % command to print the title page with above variables


%: ----------------------- cover page back side ------------------------
% Your research institution may require reviewer names, etc.
% This cover back side is required by Dresden Med Fac; uncomment if needed.


%: ----------------------- abstract ------------------------

% Your institution may have specific regulations if you need an abstract and where it is to be placed in the document. The default here is just after title.

% \include{0_frontmatter/abstract}

% The original template provides and abstractseparate environment, if your institution requires them to be separate. I think it's easier to print the abstract from the complete thesis by restricting printing to the relevant page.
% \begin{abstractseparate}
%   \input{Abstract/abstract}
% \end{abstractseparate}


%: ----------------------- tie in front matter ------------------------



%: ----------------------- contents ------------------------

\setcounter{secnumdepth}{4} % organisational level that receives a numbers
% levels are: 0 - chapter, 1 - section, 2 - subsection, 3 - subsection


%: ----------------------- list of figures/tables ------------------------


%: ----------------------- glossary ------------------------

% Tie in external source file for definitions: /0_frontmatter/glossary.tex
% Glossary entries can also be defined in the main text. See glossary.tex

\include{0_frontmatter/glossary} 
%
\begin{multicols}{2} % \begin{multicols}{#columns}[header text][space]
\begin{scriptsize} % scriptsize(7) < footnotesize(8) < small (9) < normal (10)
%
\onehalfspacing 
\printnomenclature[.9cm] % [] = distance between entry and description
\label{nom} % target name for links to glossary
%
\end{scriptsize}
\end{multicols}




%: --------------------------------------------------------------
%:                  MAIN DOCUMENT SECTION
% --------------------------------------------------------------

% the main text starts here with the introduction, 1st chapter,...
\mainmatter

% \renewcommand{\chaptername}{} % uncomment to print only "1" not "Chapter 1"


%: ----------------------- subdocuments ------------------------

% Parts of the thesis are included below. Rename the files as required.
% But take care that the paths match. You can also change the order of appearance by moving the include commands.

% \include{2/chapter_2}	% background information
% \include{5/chapter_5}
% \include{4/chapter_4}
\include{6/chapter_6}						% aims of the project




% --------------------------------------------------------------
%:                  BACK MATTER: appendices, refs,..
% --------------------------------------------------------------

% the back matter: appendix and references close the thesis


%: ----------------------- bibliography ------------------------
\renewcommand{\bibname}{References} % changes the header; default: Bibliography
\bibliography{9_backmatter/zotero} % adjust this to fit your BibTex file
\bibliographystyle{Latex/Classes/jmb} % calls style file jmb.bst
\printindex


\end{document}
